In your description of the "Right Hand Rule", is my palm to be facing toward me or away from me. I find that I have to contort my had to follow your rasmol description.
Phil bays
On Feb 15, 2004, at 6:37 PM, Miguel Howard wrote:
I would like to restart the axis orientation discussion from the beginning.
I made several incorrect statements in the previous discussion and apologize for any confusion (or lewd hand gestures :-) that I may have caused.
We are going to talk about orientation first ... rotations will be a separate discussion.
Right Hand rule says that with the right hand: thumb -> +X index finger -> +Y middle finger -> +Z
*Someone please confirm this*
RasMol/Chime have the +X axis pointing to the right, the +Y axis pointing
down, and the +Z axis pointing away from the user. This is a valid
right-hand system.
*Someone please confirm this*
There is a switch on the popup menu called 'Axes RasMol/Chime'. This
switch controls whether or not the +Y axis points down or up. By default,
this switch is 'on', for RasMol/Chime compatibility. That means that by
default, the +Y axis points down.
If you uncheck this box, then the +Y axis points upwards. The molecule is
(of course) rotated 180 degrees to reflect this.
Whether this checkbox is checked or not, the Jmol axis orientation is always right-handed.
*Someone please confirm this*
My confusion surrounding this issue is caused by the fact that
RasMol/Chime has the +Y axis pointing downwards. I find this orientation
unnatural.
Q: In the abstract, independent of any existing applications/scripts that
may exist, what do people think about this? Do you believe that the +Y
axis should point upwards or downwards?
Q: Given that there *are* existing applications and tutorials, what do you
think we should do about this issue?
Q: Do other molecular visualization applications have the +Y axis pointing
upwards or downwards?
Miguel
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